3B9G | Genus

Total Genus 121

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus	121
sequence length	317
structure length	317
Chain Sequence	SAKNVVLDHDGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVTGKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPENVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKYGEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGCPGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMGGGYAWDALTAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAENYPLTFVARNPEAEFFLDMLLRSARAC

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

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Viewer cachePut cache://localLOAD_/file/5cfe5a69bc68d412cb903735/pdb.gz

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The Resolver thinks Pdb

loadScript /static/js/j2s/core/corebio.z.js

Time for openFile(/file/5cfe5a69bc68d412cb903735/pdb.gz): 1184 ms

reading 317 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

317 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:316});backbone only;select *;

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

publication title	A Flexible Loop as a Functional Element in the Catalytic Mechanism of Nucleoside Hydrolase from Trypanosoma vivax. pubmed doi rcsb
molecule keywords	IAG-nucleoside hydrolase
molecule tags	Hydrolase
source organism	Trypanosoma vivax
total genus	121
structure length	317
sequence length	317
chains with identical sequence	B
ec nomenclature	ec 3.2.2.1: Purine nucleosidase.
pdb deposition date	2007-11-05

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01156	IU_nuc_hydro	Inosine-uridine preferring nucleoside hydrolase

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
3.90.245.10	Alpha Beta	Alpha-Beta Complex	Inosine-uridine Nucleoside N-ribohydrolase; Chain A	Ribonucleoside hydrolase-like	3b9gA00

1KIEA 3MKNA 1HOZA 1R4FA 2YHGA 3T8JA 3MKMA 4I73A 3G5IA 3EPWA 3B9GA 1YOEA 2C40A 3FZ0A 4KPNA 4KPOA 2FF2A 2MASA 1HP0A 3T8IA 3EPXA 2FF1A 4I74A 4I75A 4I72A 4P5FA 1Q8FA 1KICA 4KL0A 3B9XA 4I70A 1MASA 4WR2A 1EZRA 4I71A 5TSQA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 1KIE A;  3MKN A;  1HOZ A;  1R4F A;  2YHG A;  3T8J A;  3MKM A;  4I73 A;  3G5I A;  3EPW A;  3B9G A;  1YOE A;  2C40 A;  3FZ0 A;  4KPN A;  4KPO A;  2FF2 A;  2MAS A;  1HP0 A;  3T8I A;  3EPX A;  2FF1 A;  4I74 A;  4I75 A;  4I72 A;  4P5F A;  1Q8F A;  1KIC A;  4KL0 A;  3B9X A;  4I70 A;  1MAS A;  4WR2 A;  1EZR A;  4I71 A;  5TSQ A; 
#chains in the Genus database with same CATH topology
 1KIE A;  3MKN A;  1HOZ A;  1R4F A;  2YHG A;  3T8J A;  3MKM A;  4I73 A;  3G5I A;  3EPW A;  3B9G A;  1YOE A;  2C40 A;  3FZ0 A;  4KPN A;  4KPO A;  2FF2 A;  2MAS A;  1HP0 A;  3T8I A;  3EPX A;  2FF1 A;  4I74 A;  4I75 A;  4I72 A;  4P5F A;  1Q8F A;  1KIC A;  4KL0 A;  3B9X A;  4I70 A;  1MAS A;  4WR2 A;  1EZR A;  4I71 A;  5TSQ A; 
#chains in the Genus database with same CATH homology
 1KIE A;  3MKN A;  1HOZ A;  1R4F A;  2YHG A;  3T8J A;  3MKM A;  4I73 A;  3G5I A;  3EPW A;  3B9G A;  1YOE A;  2C40 A;  3FZ0 A;  4KPN A;  4KPO A;  2FF2 A;  2MAS A;  1HP0 A;  3T8I A;  3EPX A;  2FF1 A;  4I74 A;  4I75 A;  4I72 A;  4P5F A;  1Q8F A;  1KIC A;  4KL0 A;  3B9X A;  4I70 A;  1MAS A;  4WR2 A;  1EZR A;  4I71 A;  5TSQ A;

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similar chains in the Genus database (?% sequence similarity)

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similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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3B9GA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations